The team would successfully hold the location for five months, despite expecting to be replaced in 90 days. Over 100 of the unit was killed over this time, including Loomis and Parker. Larkin now commanded the troops. During the siege, Vargas, along with many others in the contingent, suffered deep psychological trauma. Vargas in particular suffered over the death of McGreevey even though he had not liked the man.

When Sisko along with other members of Deep Space 9 arrived on the planet to help defend AR-558, Vargas mistakenly fired on them. Vargas was on the front line during the next attack. The squad was able to hold its ground during a final attempt by the Jem'Hadar to recapture the location. Vargas, however, was stabbed in the back and killed during this attempt. (DS9: "The Siege of AR-558")